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Single Cell Genomics Reveals Plastid-Lacking Picozoa Are Close Relatives of Red Algae

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Single Cell Genomics Reveals Plastid-Lacking Picozoa Are Close Relatives of Red Algae Supplementary Information for Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae Max E. Schön, Vasily V. Zlatogursky, Rohan P. Singh, Camille Poirier, Susanne Wilken, Varsha Mathur, Jürgen F. H. Strassert, Jarone Pinhassi, Alexandra Z. Worden, Patrick J. Keeling, Thijs J. G. Ettema, Jeremy G. Wideman, Fabien Burki* List of Figures 1 Maximum Likelihood tree of the 18S rRNA gene. ........................... 3 2 Combined relative abundance of all Picozoa OTUs identified in the Tara Oceans metabarcoding data. .................................................... 4 3 Maximum likelihood tree of 794 eukaryotic species. .......................... 5 4 Support for several groupings as estimated in different trees with increasing number of fast- evolving sites removed. ......................................... 6 5 Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa. 6 6 Multi-species coalescent species tree reconstructed with ASTRAL-III. ............... 7 7 Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa. 8 8 Maximum likelihood tree of 67 eukaryotic species showing the position of Picozoa. 9 9 Complete and near complete mitochondrial genomes assembled from diverse picozoan SAGs. 10 10 Number of inferred lateral gene transfers (LGT) across a selection of 33 species. ......... 11 11 Maximum Likelihood tree of the 18S rRNA gene from the individual SAG assemblies and an extended number of reference sequences from Picozoa and other major eukaryotic groups from the PR2 database. ............................................ 12 12 Heatmap showing pairwise ANI for 43 initial picozoan SAGs as estimated with FastANI. 13 13 Boxplots of different BUSCO categories (Missing, Complete, Fragmented and Duplicated) for all selected SAGs/Co-SAGs. ........................................ 13 14 Contamination estimate for each of the 17 final SAGs/Co-SAGs. 14 15 Maximum likelihood tree of eukaryotic species showing the position of Picozoa. 15 16 Bayesian phylogenetic tree made using PhyloBayes. ......................... 16 17 Bayesian phylogenetic tree made using PhyloBayes. ......................... 17 List of Tables 1 Assembly/genome characteristics SAGs and CO-SAGs ....................... 18 1 2 Additional genomes added to the Phylogenomic dataset ....................... 18 3 Phylogenomic dataset taxon selection and taxon merging ...................... 18 4 Results from the AU and other topology tests performed with IQ-TREE . 18 5 The Picozoan MS584-11 mitochondrial genome was used as a BLAST query into the 43 picozoan SAGs. ................................................... 18 6 Commonly retained plastid pathways and proteins .......................... 18 7 EGT clustering dataset taxon selection ................................. 18 8 Phylogenomic dataset taxon selection and taxon merging ...................... 18 9 EGT and LGT results for 33 selected species/groups ......................... 18 1 untrimmed EEF2 alignment ....................................... 18 2 3 0 SAG17_NODE_209_length_6604_cov_12.631822_939-2744 2 7 'BP1' 3 0 SAG41_NODE_729_length_1138_cov_22.611165_1-553 9 SAG09_NODE_597_length_2008_cov_1.544264_102-784 SAG43_NODE_6386_length_1046_cov_569.933474_20-1046 3 2 SAG16_NODE_467_length_2239_cov_20.097664_535-2239 6 5 JX988764.1.1138_U_clone_PICOBI01F-L52R_10 4 9 1 2 KJ763213.1.1806_U_clone_SGUH612 COSAG02 SAG41_NODE_563_length_1533_cov_4.731520_304-1533 2 0 SAG35_NODE_69_length_11959_cov_32.509528_8945-10750 2 79 SAG21_NODE_816_length_2079_cov_2.398990_290-2079 6 5 SAG32_NODE_791_length_6633_cov_1359.747626_737-2542 SAG18_NODE_1586_length_1284_cov_1.328270_750-1215 8 SAG34_NODE_220_length_626_cov_0.867173_100-625 6 7 EU368003.1.1109_U_clone_FS01AA11_01Aug05_5m 9 5 EU368004.1.1126_U_clone_FS01AA94_01Aug05_5m 24 3 5 EU368020.1.1039_U_clone_FS04GA95_01Aug05_5m 100 DQ222876.1.1799_U_clone_RA000907.33 4 2 JF791041.1.1777_U_clone_7532 SAG18_NODE_3756_length_534_cov_0.671264_2-533 8 9 JX988758.1.1807_U_Picomonas_judraskeda 5 2 8 0 SAG01_NODE_1281_length_3345_cov_9.888478_301-2106 4 1 HQ867389.1.887_U_clone_SHAC701 COSAG03 SAG40_NODE_1486_length_1870_cov_3.223602_876-1870 4 5 SAG02_NODE_164_length_1182_cov_0.938135_1-1175 100 HQ869261.1.1000_U_clone_SHBA597 4 5 4 8 HQ869362.1.935_U_clone_SHBA707 41 73 SAG09_NODE_2410_length_432_cov_0.936937_1-430 KC488338.1.1714_U_clone_HL2SCM10.71 3 8 SAG36_NODE_269_length_5276_cov_1081.533127_3-1607 SAG26_NODE_716_length_5622_cov_237.617237_668-2473 6 5 SAG39_NODE_1105_length_5866_cov_172.926131_882-2687 COSAG06 5 8 SAG30_NODE_204_length_11251_cov_42.867737_1433-3238 7 9 SAG27_NODE_219_length_12917_cov_16.477298_7670-9475 5 3 JN934893.1_Picobiliphyte_SAG_sp._MS609-66 7 8 JN934890.1_Picobiliphyte_SAG_MS584-5 KJ762479.1.1805_U_clone_SGYH1057 JQ226352.1.1606_U_clone_SHAA389 3 6 4 3 KF031848.1.1765_U_clone_CC02A175.091 8 0 KJ173845.1.986_U_clone_DH117-1000m-C02 7 9100 SAG23_NODE_141_length_11148_cov_11.089963_3919-5724 COSAG04 SAG19_NODE_794_length_9268_cov_1638.280401_2687-4492 KJ173847.1.992_U_clone_DH117-1000m-C10 6 7 HQ868776.1.919_U_clone_SHAX1019 100 7 7 HQ868797.1.923_U_clone_SHAX1043 7 4 HQ868690.1.947_U_clone_SHAX927 4 0 KJ759275.1.1806_U_clone_SGYO1039 7 1 SAG08_NODE_2796_length_1578_cov_105.795132_5-1572 3 1 SAG42_NODE_33_length_26034_cov_34.003856_573-2378 SAG29_NODE_208_length_10399_cov_14.269126_3742-5547 7 0 SAG13_NODE_154_length_12455_cov_60.081013_5953-7758 COSAG01 8 4 SAG04_NODE_206_length_16512_cov_7.695729_11513-13318 6 1 9 9 SAG24_NODE_30_length_15199_cov_8.991656_4494-6299 9 0 SAG20_NODE_95_length_11004_cov_58.023107_5150-6955 SAG12_NODE_286_length_10619_cov_339.861977_9641-10619 KJ762972.1.1807_U_clone_SGUH1326 5 3 HQ869099.1.906_U_clone_SHAX616 4 5 6 3 100 HQ869574.1.909_U_clone_SHBF544 4 1 HQ869605.1.957_U_clone_SHBF578 6 1 HQ869692.1.905_U_clone_SHBF671 9 9 KC488345.1.1706_U_clone_HL5aSF04.93 JQ222911.1.1637_U_clone_SHAU435 6 6 HM561168.1.984_U_clone_CFL146DB13 3 8 SAG38_NODE_1157_length_2077_cov_56.130515_304-2077 7 2 3 8 SAG14_NODE_6_length_54255_cov_1799.083795_52455-54255 8 1 SAG06_NODE_69_length_968_cov_0.676640_12-968 SAG06_NODE_305_length_411_cov_0.810897_3-411 6 6 9 8 EU368037.1.1764_U_clone_EN351CTD039_30mN9 COSAG05 8 3 9 9 JN934891.1_Picobiliphyte_SAG_sp._MS584-11 'BP3' SAG15_NODE_683_length_4737_cov_2550.787193_738-2541 7 1 KJ173846.1.991_U_clone_DH117-1000m-C07 KJ173838.1.862_U_clone_DH113-5m-D02 100 DQ222875.1.1801_U_clone_OR000415.159 6 7 100 JN934892.1_Picobiliphyte_SAG_sp._MS584-22 HQ867491.1.910_U_clone_SHAH476 9 9 HQ867421.1.875_U_clone_SHAC745 7 1 8 1 KF130491.1.1763_U_clone_ST8360.104 SAG22_NODE_175_length_16235_cov_67.112729_1670-3473 8 5 9 8 DQ222874.1.1786_U_clone_HE001005.148 JX988767.1.1135_U_clone_PICOBI02F-L52R_He 9 9 EU368021.1.1096_U_clone_FS04GA46_01Aug05_5m 100 9 3 AY426835.1.1803_U_clone_BL000921.8 SAG31_NODE_544_length_14245_cov_68.376644_6887-8690 'BP2' 8 0 HQ869075.1.930_U_clone_SHAX587 8 2 100 100 JX840937.1.1271_U_clone_ARK_21 KJ173843.1.991_U_clone_DH116-100m-C03 'Deep branching Picozoa 1' KJ173850.1.854_U_clone_DH117-1000m-D03 7 4 100 KJ763562.1.1796_U_clone_SGYP1354 SAG11_NODE_229_length_11945_cov_77.865187_857-2654 8 9 6 0 DQ060528.1.800_U_clone_NOR50.25 100 DQ060527.1.1237_U_clone_NOR50.52 9 2 KC488340.1.1697_U_clone_HL5aSCM04.10 9 8 HM561172.1.953_U_clone_CFL119DB12 8 8 6 6 KJ762470.1.1800_U_clone_SGYH1041 'Deep branching Picozoa 2' 100 KC488342.1.1710_U_clone_HL5aSCM04.38 HQ868882.1.878_U_clone_SHAX1135 KC488336.1.1682_U_clone_BBL1SF10.02 9 9 HQ867420.1.880_U_clone_SHAC744 5 7 8 6 HQ867337.1.876_U_clone_SHAC623 5 0 HQ867471.1.868_U_clone_SHAC426 4 6 8 9 AY343928.1.1812_U_clone_He000803-72 2 2 KJ759623.1.1791_U_clone_SGYO702 KC488339.1.1675_U_clone_HL2SF10.08 5 6 GU824414.1.1057_U_clone_AA5F13RM2D10 7 5 100 HQ867331.1.869_U_clone_SHAC614 4 7 HQ867442.1.871_U_clone_SHAC390 3 5 DQ060524.1.1778_U_clone_NW414.27 SAG28_NODE_1308_length_928_cov_36.342746_1-913 7 1 HQ866220.1.881_U_clone_SGSP644 8 1 7 3 HQ869572.1.881_U_clone_SHBF542 KC488334.1.1687_U_clone_BBL1SCM04.08 9 9 100 EU561759.1.879_U_clone_IND31.88 KJ759641.1.1788_U_clone_SGYO733 HQ867427.1.876_U_clone_SHAC752 8 9 FN689854.1.826_U_clone_He040503_11A HQ864893.1.880_U_clone_SGPX462 100 U53126.1.1756_U_strain_CCMP_325_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Hanusia_Hanusia_phi 6 9 4 3 X57162.1.1773_U__Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Guillardia_Guillardia_theta 7 2 L28811.1.1763_U_strain_CCAP_977_2a_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Cryptomonas_Cryptomonas_paramecium 9 2 HM126532.1.1732_U_strain_K-1487_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Rhodomonas_Rhodomonas_salina 8 3 AJ007285.1.1761_U_strain_CCMP_704_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Proteomonas_Proteomonas_sulcata 9 7 AM901350.1.1670_U_strain_CCMP_441_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Hemiselmis_Hemiselmis_andersenii JF790986.1.1777_U_clone_1126_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Cryptomonadales_Cryptomonadales_X_Geminigera_Geminigera_cryophila AF508277.1.1721_U_strain_CCMP1869_Eukaryota_Hacrobia_Cryptophyta_Cryptophyceae_Goniomonadales_Goniomonadales_X_Goniomonas_Goniomonas_pacifica 100 HQ191366.1.1830_U_clone_PA2009C5_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp. 9 9 2 7 GU068005.1.1774_U_clone_ESS241006.012_Eukaryota_Hacrobia_Katablepharidophyta_Katablepharidaceae_Katablepharidales_Katablepharidales_X_Katablepharidales_XX_Katablepharidales_XX_sp.
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